Note: This is a discussion about building the most efficient ship possible, it doesn't have to look good just be the most bang for its buck. Following the guide you will likely beat the bounty mode ships with ease as these are designed with flaws in mind.
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Roles & Tactics
When I tried to design ships I noticed that I build most in four different ways.
1. Frontside Ships
Frontside vessel mount most of their weapons at the prow.
Favoured weapons: Cannons, eBolts and lasers, possibly ion beams and side mounted missiles
Strengths: All weapons and shields face forward, giving it tremendous firepower, able to chew through everything in it´s prize class. Generally fast as most engines face backwards and mount cannons, lasers and eBolts.
Weaknesses: Forward facing shields leave it open to attacks from the sides and rear though, having only little armor to protect the inside. While you can somewhat rotate the ships to distribute incoming fire on shields it is far less effective than on broadside desgins.

2. Broadside Ships
Broadside vessels mount two or more (like cubes) of their sides with weapons.
Favoured weapons: Cannons, eBolts and lasers
Strengths: They are armored and shielded all around, making them tough opponents and much better against multiple small targets or in fleet actions. They can rotate the ship so that incoming fire is absorbed by shields and gives them time to regenerate.
Weaknesses: Compared to frontal assault ships they have fewer weapons on each side, leaving salvos smaller. Eninges are crucial weak points as once the ship stops rotating it can be taken down quicker.

3. Diagonal Ships (by Ohm)
Diagonal vessels have weapons on their sides and no frontside. They can be used as both frontside and broadside vessels.
Favoured weapons: Cannons, eBolts and lasers (missiles)
Strengths: When angled right they can fire with cannons and lasers on both sides. Their shields provide better coverage to weapons behind using not only the front but also the side parts.
Weaknesses: If the nose comes under heavy fire and they need to turn they can only bring one broadside to bear. They are also more difficult to construct and the AI doesn't handle them very well, making manual alignment necessary.

4. Ranged Vessels
Favoured weapons: Ion beams and missiles ( I found that large cannons are too unreliable in hitting as the projectile is quite slow)
Strengths: These fast ships constantly stay at maximum distance so as not to get caught by large pursuers. They can carry large amounts of missiles to overwhelm PD or use their ion beams on an enemy unable to fire back.
Weaknesses: If the vessel get caught they are toast because they are only lightly armored due to mass constraints.

5. Fighter swarms (& hopefully carriers sometime)
Favoured weapons: Ion beams (AI is very good at using those and staying at max distance); Cannons, eBolts and lasers for melee ships
Strengths: Multiple smaller ships are extremely effective as the can surround targets and prey on their weaknesses better. They are fast and while not the toughest opponents can kill most larger vessels when facing an equally costly combatant.
Weaknesses: Defences are likely to be lackluster especially against front, broadside ships and missiles.

Design Principles
There is a difference in priorities between designing small ships (<200k), medium ships and large ships (> 1kk). The larger the ship the less you want to place reactors near the outside and have to resort to storage and conveyors.
Weapons
For a review of weapons you can look here. Link
Ammo to Weapon Ratio
- Energy weapons: Lasers need 1/6, eBolts 1/3 and Ion beams 5/6 of a reactor to work continuously. Make sure there are enough.
- Medium cannons: The optimal ratio is 3:2 factories but 2:1 is still good. Keep Minimize walk ways in mind!
- Large cannons have a 3:4 factories ratio but their DPS only drops by ~10% with 1:1.
- For missiles 2:1 factories is practical, maybe less depending on walk time. While a 1:1 ratio would be optimal, the high cost of factories makes missile storage a good substitute for volley fire (i.e. 8 missiles, 4 factories & 4 storage facilities means a volley every ~14 seconds.) If the ship is used by AI a 1:1 ratio is best for continuous missile spam (though it is not very cost effective doing so.)
Ship Optimization
While iterating through ship designs I noticed things that made my ships a lot tougher:
Armoring: Stopping those pesky cannons from eating your ships innards is a good way to design your ship. It is noteworthy that weapons also stop cannon penetration. You don't always need full blocks everywhere but even a half block or a triangle can absorb some hit and weighs much less. Armor weighs 3x as much as a normal section of the ship.
Center of Mass: For the rotation of the ship it is important that all parts are as close to the center as possible and the engines as far away as possible. (see Role 5, ion swarm ship)
Crew Quarters: Try to place them where the are needed (i.e. near reactors, storage and factories), so they can immediatly leap into action. A long delay can lead to ammo shortages and shield failures!
Corridors are important so the passages don't get congested. If crew walks through rooms or other people, they do so at 1/2 the speed, if both at 1/4. Although I dislike wasting space, two way corridors can heavily improve traffic flow.
Minimize walk ways: This is as important for weapons as for shields. Ditch your ammo storage and replace it with factories. They have to be directly connected to the cannons or the DPS will drop by 30-50% if they are 1 or 2 corridors away! For small ships place power plants directly connected to shields and they will charge at a tremendous rate. Larger ships can do this with power storage.
Shield Armoring: putting armor in front of the shield generator protects the shield even when it goes down and recharges for a while. This makes the ship much more durable. It may not always be possible but generally it´s advisable. (see Role 2, Broadside Vessel)
- Shield Overlapping: Getting shields to overlap weapons is the most efficient way to protect your DPS. Generally, I found that two or three overlapping shields are best as more can get different to lay out or costly. (see Role 2, Broadside Vessel)
Construction Tips
- Mirror mode is your friend. It makes construction much faster.
- Use the tool (T) to move or copy sections of your ship.
- Plan your sections out beforehand. It helps me to create examples of what i want to do (like how to lay out weapon positions then shield & armor them and see if it is workable) then copy the sections into my ship.
Conclusion
While no ship can be perfect in every way it is good to keep ship roles and desgin principles in mind.
What are your opinions? Have you found other roles or principles? Do you have tips for your fellow star ship builders?